chr5-86038135-T-A

Variant names:

• chr5-86038135-T-A
• rs2974097

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.504 in 151,966 control chromosomes in the GnomAD database, including 20,495 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.50 (20495 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76522 AN: 151848 Hom.: 20466 Cov.: 32

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.501

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.504 AC: 76594 AN: 151966 Hom.: 20495 Cov.: 32 AF XY: 0.504 AC XY: 37428 AN XY: 74268

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.494

Alfa AF: 0.312 Hom.: 704

Bravo AF: 0.520

Asia WGS AF: 0.291 AC: 1010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.35

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2974097; hg19: chr5-85333953;